PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity

<p>Abstract</p> <p>Background</p> <p>Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents a challenge for phage identification and characterization, especially in environmental samples where it is difficult to culture phage-host systems. Homologous conserved genes (or "signature genes") present in groups of closely-related phages can be used to explore phage diversity and define evolutionary relationships amongst these phages. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers to amplify those genes from environmental samples; however, there is currently no existing computational tool that biologists can use for this purpose.</p> <p>Results</p> <p>Here we present PhiSiGns, a web-based and standalone application that performs a pairwise comparison of each gene present in user-selected phage genomes, identifies signature genes, generates alignments of these genes, and designs potential PCR primer pairs. PhiSiGns is available at (<url>http://www.phantome.org/phisigns/</url>; <url>http://phisigns.sourceforge.net/</url>) with a link to the source code. Here we describe the specifications of PhiSiGns and demonstrate its application with a case study.</p> <p>Conclusions</p> <p>PhiSiGns provides phage biologists with a user-friendly tool to identify signature genes and design PCR primers to amplify related genes from uncultured phages in environmental samples. This bioinformatics tool will facilitate the development of novel signature genes for use as molecular markers in studies of phage diversity, phylogeny, and evolution.</p

Study of W boson production in PbPb and pp collisions at sqrt(s[NN]) = 2.76 TeV

A measurement is presented of W-boson production in PbPb collisions carried out at a nucleon-nucleon (NN) centre-of-mass energy sqrt(s[NN]) of 2.76 TeV at the LHC using the CMS detector. In data corresponding to an integrated luminosity of 7.3 inverse microbarns, the number of W to mu mu-neutrino decays is extracted in the region of muon pseudorapidity abs(eta[mu])<2.1 and transverse momentum pt[mu]>25 GeV. Yields of muons found per unit of pseudorapidity correspond to (159 +/- 10 (stat.) +/- 12 (syst.)) 10E-8 W(plus) and (154 +/- 10 (stat.) +/- 12 (syst.)) 10E-8 W(minus) bosons per minimum-bias PbPb collision. The dependence of W production on the centrality of PbPb collisions is consistent with a scaling of the yield by the number of incoherent NN collisions. The yield of W bosons is also studied in a sample of pp interactions at sqrt(s)= 2.76 TeV corresponding to an integrated luminosity of 231 inverse nanobarns. The individual W(plus) and W(minus) yields in PbPb and pp collisions are found to agree, once the neutron and proton content in Pb nuclei is taken into account. Likewise, the difference observed in the dependence of the positive and negative muon production on pseudorapidity is consistent with next-to-leading order perturbative QCD calculations.Comment: Submitted to Physics Letters

The dominant Anopheles vectors of human malaria in the Asia-Pacific region: occurrence data, distribution maps and bionomic précis

<p>Abstract</p> <p>Background</p> <p>The final article in a series of three publications examining the global distribution of 41 dominant vector species (DVS) of malaria is presented here. The first publication examined the DVS from the Americas, with the second covering those species present in Africa, Europe and the Middle East. Here we discuss the 19 DVS of the Asian-Pacific region. This region experiences a high diversity of vector species, many occurring sympatrically, which, combined with the occurrence of a high number of species complexes and suspected species complexes, and behavioural plasticity of many of these major vectors, adds a level of entomological complexity not comparable elsewhere globally. To try and untangle the intricacy of the vectors of this region and to increase the effectiveness of vector control interventions, an understanding of the contemporary distribution of each species, combined with a synthesis of the current knowledge of their behaviour and ecology is needed.</p> <p>Results</p> <p>Expert opinion (EO) range maps, created with the most up-to-date expert knowledge of each DVS distribution, were combined with a contemporary database of occurrence data and a suite of open access, environmental and climatic variables. Using the Boosted Regression Tree (BRT) modelling method, distribution maps of each DVS were produced. The occurrence data were abstracted from the formal, published literature, plus other relevant sources, resulting in the collation of DVS occurrence at 10116 locations across 31 countries, of which 8853 were successfully geo-referenced and 7430 were resolved to spatial areas that could be included in the BRT model. A detailed summary of the information on the bionomics of each species and species complex is also presented.</p> <p>Conclusions</p> <p>This article concludes a project aimed to establish the contemporary global distribution of the DVS of malaria. The three articles produced are intended as a detailed reference for scientists continuing research into the aspects of taxonomy, biology and ecology relevant to species-specific vector control. This research is particularly relevant to help unravel the complicated taxonomic status, ecology and epidemiology of the vectors of the Asia-Pacific region. All the occurrence data, predictive maps and EO-shape files generated during the production of these publications will be made available in the public domain. We hope that this will encourage data sharing to improve future iterations of the distribution maps.</p

Synthesis, Micelle Formation, and Bulk Properties of Poly(ethylene glycol)-b-Poly(pentafluorostyrene)-g-polyhedral Oligomeric Silsesquioxane Amphiphilic Hybrid Copolymers

The synthesis, micelle formation, and bulk properties of semifluorinated amphiphilic poly(ethylene glycol)-b-poly-(pentafluorostyrene)-g-cubic polyhedral oligomeric silsesquioxane (PEG-b-PPFS-g-POSS) hybrid copolymers is reported. The synthesis of amphiphilic PEG-b-PPFS block copolymers are achieved using atom transfer radical polymerization (ATRP) at 100 degrees C in trifluorotoluene using modified poly(ethylene glycol) as a macroinitiator. Subsequently, a proportion of the reactive para-F functionality on the pentafluorostyrene units was replaced with aminopropylisobutyl POSS through aromatic nucleophilic substitution reactions. The products were fully characterized by H-1-NMR and GPC. The products, PEG-b-PPFS and PEG-b-PPFS-g-POSS, were subsequently self-assembled in aqueous solutions to form micellar structures. The critical micelle concentrations (cmc) were estimated using two different techniques: fluorescence spectroscopy and dynamic light scattering (DLS). The cmc was found to decrease concomitantly with the number of POSS particles grafted per copolymer chain. The hydrodynamic particle sizes (R-h) of the micelles, calculated from DLS data, increase as the number of POSS molecules grafted per copolymer chain increases. For example, Rh increased from similar to 60 nm for PEG-b-PPFS to similar to 80 nm for PEG-b-PPFS-g-POSS25 (25 is the average number of POSS particles grafted copolymer chain). Static light scattering (SLS) data confirm that the formation of larger micelles by higher POSS containing copolymers results from higher aggregation numbers (N-agg), caused by increased hydrophobicity. The R-g/R-h values, where R-g is the radius of gyration calculated from SLS data, are consistent with a spherical particle model having a core-shell structure. Thermal characterization by differential scanning calorimetry (DSC) reveals that the grafted POSS acts as a plasticizer; the glass transition temperature (T-g) of the PPFS block in the copolymer decreases significantly with increasing POSS content. Finally, the rhombohedral crystal structure of POSS in PEG-b-PPFS-g-POSS was verified by wide angle X-ray diffraction measurements. (C) 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 152-163, 201

Advancing Environmental Health Literacy: Validated Scales of General Environmental Health and Environmental Media-Specific Knowledge, Attitudes and Behaviors

Environmental health literacy (EHL) involves understanding and using environmental information to make decisions about health. This study developed a validated survey instrument with four scales for assessing media-specific (i.e., air, food, water) and general EHL. The four scales were created as follows: 1) item generation: environmental health scientists and statisticians developed an initial set of items in three domains: knowledge, attitudes, and behaviors; 2) item review: items were reviewed for face validity; 3) validation: 174 public health students, the exploratory sample, and 98 community members, the test sample, validated the scales. The scales&rsquo; factor structure was based on exploratory factor analysis (EFA) and model fit was assessed through confirmatory factor analysis (CFA). For each scale, the final EFA resulted in an independent three-factor solution for knowledge, attitudes, and behaviors. Good fit for the three-factor structure was observed. Model fit for CFA was generally confirmed with fit indices. The scales showed internal consistency with Cronbach&rsquo;s alpha from 0.63 to 0.70. The 42-item instrument represents an important contribution towards assessing EHL and is designed to enable meaningful engagement between researchers and community members about environmental health. The intended outcome is sustained community&ndash;academic partnerships benefiting research design, implementation, translation, dissemination, and community action